https://github.com/khanlab/hippunfold

BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)

deep-learning hippocampus mri python segmentation

Last synced: 14 Dec 2025

https://github.com/khanlab/zarrnii

Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations

lightsheet-microscopy mri nifti ome-zarr spim transformations zarr

Last synced: 28 Apr 2026

https://github.com/khanlab/tar2bids

Last synced: 05 Feb 2026

https://github.com/khanlab/labelmerge

Merge label maps

Last synced: 05 Feb 2026

https://github.com/khanlab/scattr

BIDS app for structural connectivity between targeted regions

Last synced: 05 Feb 2026

https://github.com/khanlab/kslurm

Helper scripts and wrappers for running commands on SLURM compute clusters.

cli compute-clusters python slurm

Last synced: 05 Feb 2026

https://github.com/khanlab/neuroglia-helpers

Helper and wrapper scripts for using Singularity locally and on compute canada

Last synced: 05 Feb 2026

https://github.com/khanlab/autobids

Automated Dicom to BIDS and pipelines using compute canada

Last synced: 29 Apr 2025

https://github.com/khanlab/cfmm2tar

Tools for dicom-server retrieval, tarballing and conversion to bids

Last synced: 27 Feb 2026

https://github.com/khanlab/funcmasker-flex

BIDS App for U-net brain masking of fetal bold MRI

bids bold masking mri unet

Last synced: 05 Feb 2026

https://github.com/khanlab/snakedwi

Last synced: 05 Feb 2026

https://github.com/khanlab/khanlab.github.io

Khan Lab website

Last synced: 05 Feb 2026

https://github.com/khanlab/hippunfold-atlases

Surface-based atlases for hippunfold v2.x

Last synced: 05 Feb 2026

https://github.com/khanlab/actions

Centralized repo of reusable GH actions

Last synced: 05 Feb 2026

https://github.com/khanlab/cvpl_tools

A Python package for utilities and classes related to the file I/O, dataset record keeping for image processing and computer vision.

Last synced: 05 Feb 2026

https://github.com/khanlab/imaris_ims_zarr

Imaris file format reader

Last synced: 21 Jun 2026

https://github.com/khanlab/dicom2tar

Tool for gathering dicom files into organized tarballs, each containing unique study instance

Last synced: 08 Apr 2026

https://github.com/khanlab/hippunfold_deps

Dependencies container for hippocampal_autotop (niftynet, minified fsl/ants, c3d, mcr)

Last synced: 05 Feb 2026

https://github.com/khanlab/gradcorrect

BIDS app for correcting gradient non-linearities, saves corrected images as mirrored BIDS dataset, along with warp and intensity-correction fields

Last synced: 05 Feb 2026

https://github.com/khanlab/diffparc-surf

Snakebids app for diffparc-surf, including dwi processing

Last synced: 05 Feb 2026

https://github.com/khanlab/tar2bids-heuristics

Study heuristics for autobids

Last synced: 05 Feb 2026

https://github.com/khanlab/wiki

Last synced: 05 Feb 2026

https://github.com/khanlab/hippunfold-plot

Plotting functions for hippocampal surface maps from HippUnfold

Last synced: 05 Feb 2026

https://github.com/khanlab/autobids-portal

Last synced: 05 Feb 2026

https://github.com/khanlab/anatprep

Anatomical preprocessing snakebids app for TRIDENT (15T) mouse data

Last synced: 21 Jun 2026